Grokbase Groups R r-help June 2016
Hi all,

I used R package "haplo.stats" to see if the haplotype in my data has any effect on the trait, with the genotype, age, height and

weight as the predictor and trait as the response. I used the following code:

fit.gaus <- haplo.glm(y ~ age + height + weight + geno.glm, family=gaussian,, na.action="na.geno.keep", x=TRUE, control=haplo.glm.control(haplo.freq.min=.02))

But R showed me this error:

  Warning message:

In haplo.glm(y ~ age + height + weight + geno.glm, family = gaussian, :

   Failed to converge during EM-glm loop

What does it mean that failed to converge during EM-glm loop? I wonder if there is anything wrong with my command?

Thank you for your attention, I am looking forward to your reply.


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  • Ravi Varadhan at Jun 14, 2016 at 3:56 pm
    It is a "warning" message, but not an "error" message. Therefore, you should still get parameter estimates. However, lack of convergence is often an important issue. Although in the case of the EM algorithm, it may not be so serious since EM is notoriously slow to converge when you set a small tolerance for convergence. You may fiddle with the control options for EM algorithm and see if you can get convergence. If not, you should contact the package authors.

    Hope this is helpful,

    Ravi Varadhan, Ph.D. (Biostatistics), Ph.D. (Environmental Engg)
    Associate Professor, Department of Oncology
    Division of Biostatistics & Bionformatics
    Sidney Kimmel Comprehensive Cancer Center
    Johns Hopkins University
    550 N. Broadway, Suite 1111-E
    Baltimore, MD 21205

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postedJun 13, '16 at 3:22p
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